Constructing a broadly inclusive seed plant phylogeny.

By Stephen A. Smith, Joseph W. Brown. American-Eurasian journal of botany, 2018

953 citations recorded by the source corpus.

PREMISE OF THE STUDY Large phylogenies can help shed light on macroevolutionary patterns that inform our understanding of fundamental processes that shape the tree of life. These phylogenies also serve as tools that facilitate other systematic, evolutionary, and ecological analyses. Here we combine genetic data from public repositories (GenBank) with phylogenetic data (Open Tree of Life project) to construct a dated phylogeny for seed plants. METHODS We conducted a hierarchical clustering analysis of publicly available molecular data for major clades within the Spermatophyta. We constructed phylogenies of major clades, estimated divergence times, and incorporated data from the Open Tree of Life project, resulting in a seed plant phylogeny. We estimated diversification rates, excluding those taxa without molecular data. We also summarized topological uncertainty and data overlap for each major clade. KEY RESULTS The trees constructed for Spermatophyta consisted of 79,881 and 353,185 terminal taxa; the latter included the Open Tree of Life taxa for which we could not include molecular data from GenBank. The diversification analyses demonstrated nested patterns of rate shifts throughout the phylogeny. Data overlap and inference uncertainty show significant variation throughout and demonstrate the continued need for data collection across seed plants. CONCLUSIONS This study demonstrates a means for combining available resources to construct a dated phylogeny for plants. However, this approach is an early step and more developments are needed to add data, better incorporating underlying uncertainty, and improve resolution. The methods discussed here can also be applied to other major clades in the tree of life.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/6b1d23259c0d31822b07123887a53769b25e1a49

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In Ecology, Evolution, Behavior and Systematics

1. Yi Jin
2. Hong Qian
3. C. Koenig
4. H. Kreft
5. Patrick Weigelt
6. Tao Deng
7. Fabien Leprieur
8. Xianli Wang

In Molecular Biology

1. Hong Qian
2. Yi Jin
3. H. Kreft

In Plant Science

1. Yi Jin
2. Patrick Weigelt
3. Hong Qian
4. C. Koenig
5. H. Kreft
6. D. Jablonski

Citations in the corpus

• Geographic patterns and environmental correlates of taxonomic and phylogenetic beta diversity for large‐scale angiosperm assemblages in China (2020, methodology): “Specifically, V.PhyloMaker uses an updated and expanded version of the dated megaphylogeny GBOTB reported by Smith and Brown (2018) as a backbone to generate phylogenies.”
• V.PhyloMaker2: An updated and enlarged R package that can generate very large phylogenies for vascular plants (2022, methodology): “Phylogenetic trees serve as tools that facilitate systematic, evolutionary and ecological analyses (Smith and Brown, 2018).”
• GIFT – A Global Inventory of Floras and Traits for macroecology and biogeography (2019, background): “In combination with functional traits from the botanical literature or large trait databases (e.g. RBG Kew, 2008; Kattge et al., 2011b) and ever-growing species-level phylogenies (e.g. Smith & Brown, 2018), this represents a promising basis for macroecological and biogeographic research.”